GSM6771440: 970, BruUV-seq, EtOH, 3; Mus musculus; OTHER
Cells were lysed directly in TRIzol followed by isolation of total RNA. The isolated total RNA was further treated with DNAse (TURBO DNA-free Kit; Invitrogen) and a spike-in cocktail of Bru-labeled and unlabeled RNA was mixed in with total RNA. Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences). Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2014; Paulsen et al., 2013), but with the following modifications. Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first strand synthesis. A universal ligation adapter and dual-index, barcoded primers were used for PCR. Size selection for all libraries was via agarose gel excision.